chore: install Bracken module

modules.json

@@ -21,6 +21,10 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
+                    "bracken/bracken": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"

modules/nf-core/bracken/bracken/main.nf

@@ -0,0 +1,45 @@
+process BRACKEN_BRACKEN {
+    tag "$meta.id"
+    label 'process_low'
+
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
+        'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
+
+    input:
+    tuple val(meta), path(kraken_report)
+    path database
+
+    output:
+    tuple val(meta), path(bracken_report), emit: reports
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def threshold = meta.threshold ?: 10
+    def taxonomic_level = meta.taxonomic_level ?: 'S'
+    def read_length = meta.read_length ?: 150
+    def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    bracken_report = "${prefix}_${taxonomic_level}.tsv"
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    def VERSION = '2.7'
+    """
+    bracken \\
+        ${args} \\
+        -d '${database}' \\
+        -i '${kraken_report}' \\
+        -o '${bracken_report}'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bracken: ${VERSION}
+    END_VERSIONS
+    """
+}

modules/nf-core/bracken/bracken/meta.yml

@@ -0,0 +1,45 @@
+name: bracken_bracken
+description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
+keywords:
+  - sort
+tools:
+  - bracken:
+      description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
+      homepage: https://ccb.jhu.edu/software/bracken/
+      documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
+      tool_dev_url: https://github.com/jenniferlu717/Bracken
+      doi: "10.7717/peerj-cs.104"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - kraken_report:
+      type: file
+      description: TSV file with six columns coming from kraken2 output
+      pattern: "*.{tsv}"
+  - database:
+      type: file
+      description: Directory containing the kraken2/Bracken files for analysis
+      pattern: "*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reports:
+      type: file
+      description: TSV output report of the re-estimated abundances
+      pattern: "*.{tsv}"
+
+authors:
+  - "@Midnighter"